Nuclear and Mitochondrial Gene Data Support Recent Radiation within the Sea Spider Species Complex Pallenopsis patagonica

AbstractRelationships of Mabuya lizards from the islands of the Gulf of Guinea where estimated using partial 12S rRNA, 16S rRNA and cytochrome b mitochondrial gene sequences. Mabuya maculilabris from São Tomé and Principe are discreet monophyletic units, highly divergent from each other and from mainland populations, indicating M. maculilabris may be a species complex. Mabuya affinis from Principe is similarly distinct from mainland populations of this species. The relationships of Mabuya ozorii from Annobon are unclear, but the three species in the Gulf of Guinea islands are not closely related, indicating multiple independent colonization events. The recent proposal to partition Mabuya into four genera is premature, since at least five distinct genetic lineages can be identified.

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Taxonomy and phylogeny of Pluteus glaucotinctus sensu lato (Agaricales, Basidiomycota), a multicontinental species complex

Phytotaxa ◽

10.11646/phytotaxa.188.2.2 ◽

2014 ◽

Vol 188 (2) ◽

pp. 78 ◽

Cited By ~ 3

Author(s):

Nelson Menolli Jr. ◽

ALFREDO JUSTO ◽

PEDRO ARRILLAGA ◽

C. K. PRADEEP ◽

ANDREW M. MINNIS ◽

...

Keyword(s):

Dna Sequence ◽

Species Delimitation ◽

Species Complex ◽

Democratic Republic ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sensu Stricto ◽

Type Collection ◽

Data Support ◽

Republic Of The Congo

In order to better understand species delimitation in the Pluteus glaucotinctus species complex, we present a detailed study based on morphological and DNA sequence (nrITS + tef1) data. Pluteus glaucotinctus sensu stricto is known only from the type collection (Democratic Republic of the Congo), which is re-examined here. Four other species are recognized in this complex and described herein as new: P. izurun from Spain, P. meridionalis from Brazil, P. padanilus from India and P. thoenii from Africa. Phylogenetic analyses based on nrITS + tef1 sequence data support the recognition of all species in this complex.

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Genetic data support independent glacial refugia and open ocean barriers to dispersal for the Southern Ocean sea spider Austropallene cornigera(Möbius, 1902)

Journal of Crustacean Biology ◽

10.1163/1937240x-00002351 ◽

2015 ◽

Vol 35 (4) ◽

pp. 480-490 ◽

Cited By ~ 22

Author(s):

Jana Sophie Dömel ◽

Florian Leese ◽

Peter Convey

Keyword(s):

Southern Ocean ◽

Genetic Data ◽

Glacial Refugia ◽

Open Ocean ◽

Data Support ◽

Sea Spider

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Identifying spiders through DNA barcodes

Canadian Journal of Zoology ◽

10.1139/z05-024 ◽

2005 ◽

Vol 83 (3) ◽

pp. 481-491 ◽

Cited By ~ 308

Author(s):

Rowan D.H Barrett ◽

Paul D.N Hebert

Keyword(s):

Mating Systems ◽

Mitochondrial Gene ◽

Model Systems ◽

Dna Barcodes ◽

Cytochrome C Oxidase I ◽

Accurate Identification ◽

Spider Species ◽

Taxonomic Impediment ◽

Gene Coding ◽

Identification Tool

With almost 40 000 species, the spiders provide important model systems for studies of sociality, mating systems, and sexual dimorphism. However, work on this group is regularly constrained by difficulties in species identification. DNA-based identification systems represent a promising approach to resolve this taxonomic impediment, but their efficacy has only been tested in a few groups. In this study, we demonstrate that sequence diversity in a standard segment of the mitochondrial gene coding for cytochrome c oxidase I (COI) is highly effective in discriminating spider species. A COI profile containing 168 spider species and 35 other arachnid species correctly assigned 100% of subsequently analyzed specimens to the appropriate species. In addition, we found no overlap between mean nucleotide divergences at the intra- and inter-specific levels. Our results establish the potential of COI as a rapid and accurate identification tool for biodiversity surveys of spiders.

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New species of Moenkhausia Eigenmann, 1903 (Characiformes: Characidae) with comments on the Moenkhausia oligolepis species complex

Neotropical Ichthyology ◽

10.1590/s1679-62252009000200005 ◽

2009 ◽

Vol 7 (2) ◽

pp. 161-168 ◽

Cited By ~ 44

Author(s):

Ricardo C. Benine ◽

Tatiane C. Mariguela ◽

Claudio Oliveira

Keyword(s):

New Species ◽

Lateral Line ◽

Species Complex ◽

Mitochondrial Gene ◽

Single Species ◽

Genetic Distances ◽

Similar Species ◽

Body Coloration ◽

Three Samples ◽

High Genetic Distance

A new species of Moenkhausia is described from tributaries of the rio Paraguay, Brazil. The new species is diagnosed from congeners by characters related to body coloration, the number of lateral line scales, the degree of poring of the lateral line, and number of scales rows above and below the lateral line. Molecular analyses using partial sequences of the mitochondrial gene Cytochrome Oxidase I from specimens of the new species and specimens belonging to morphologically similar species demonstrated that the new species is easily differentiated by their high genetic distance and by their position in the phylogenetic hypothesis obtained through the Maximum Parsimony methodology. The analyses of three samples of M. oligolepis also revealed that they have high genetic distances and belong to different monophyletic groups suggesting that this species corresponds to a species complex rather than a single species.

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Phylogeography of the Habronattus amicus species complex (Araneae: Salticidae) of western North America, with evidence for localized asymmetrical mitochondrial introgression

Zootaxa ◽

10.11646/zootaxa.2307.1.2 ◽

2009 ◽

Vol 2307 (1) ◽

pp. 39-60 ◽

Cited By ~ 8

Author(s):

MARSHAL HEDIN ◽

MICHAEL C. LOWDER

Keyword(s):

North America ◽

Species Complex ◽

Mitochondrial Gene ◽

Microhabitat Use ◽

Nominal Species ◽

Western North America ◽

Ecological Data ◽

Dune Systems ◽

South Central ◽

Mitochondrial Introgression

The frequency and significance of hybridization and gene introgression in spiders (Araneae) is unclear, largely because few studies have combined multiple lines of evidence in the study of systems where introgression is likely. Here we consider multiple types of data to gauge the prevalence and importance of mitochondrial introgression for three species of the Habronattus amicus species complex distributed in western North America. A comprehensive phylogeographic sample recovers some geographically-coherent mitochondrial clades, but conspicuously fails to resolve nominal species as monophyletic. This pattern of discordance between molecules and morphological taxonomy is studied in more detail for two species, H. amicus (Peckham and Peckham) and H. ustulatus (Griswold), found in syntopy on three dune systems in south-central Oregon. Here, multivariate morphological analyses clearly distinguish these two species, but also reveal a narrow window of size overlap between small H. amicus females and large H. ustulatus males. A quantitative assessment of microhabitat use shows that these species occupy different microhabitats at two of three dune systems, but that this difference breaks down at a single site (Summer Lake). Consistent with the size overlap and ecological data, mitochondrial data suggest interspecific gene flow at Summer Lake, which is apparently asymmetric from H. amicus into H. ustulatus. The introgression dynamics revealed in south-central Oregon impact our interpretation of mitochondrial gene trees for the entire species complex, and provide important insight into how hybridization may be influencing evolution in this diverse spider genus.

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Species composition and hybridisation of mussel species (Bivalvia: Mytilidae) in Australia

Marine and Freshwater Research ◽

10.1071/mf15307 ◽

2016 ◽

Vol 67 (12) ◽

pp. 1955 ◽

Cited By ~ 8

Author(s):

Emi S. Ab Rahim ◽

Thuy T. T. Nguyen ◽

Brett Ingram ◽

Cynthia Riginos ◽

Kim J. Weston ◽

...

Keyword(s):

Molecular Markers ◽

Species Composition ◽

Mytilus Edulis ◽

Southern Hemisphere ◽

Northern Hemisphere ◽

Species Complex ◽

Mytilus Galloprovincialis ◽

Mitochondrial Gene ◽

Marker System ◽

Single Marker

Mussels belonging to the Mytilus edulis species complex have been the focus of numerous studies exploring the systematics and origin of this commercially and ecologically important genus. Species have wide geographical ranges and hybridise where their distributions overlap, making identification difficult. Several molecular markers have been used to distinguish between the species within the M. edulis species complex; however, no single marker system has been found to be completely diagnostic, and a combination of markers are used. Here, we used a combination of three nuclear genes and a mitochondrial gene region to assess the species composition of Mytilus mussels collected across its geographical range in Australia. Our results show that the majority (98.5%) of individuals sampled from Australian populations are Mytilus galloprovincialis, with 56.2% of them displaying a southern hemisphere haplotype, 10.3% displaying a putatively northern hemisphere haplotype, and 32% having M. galloprovincialis genotypes consistent with either northern or southern hemisphere M. galloprovincialis lineages. The taxonomic origin of the remaining 1.5% of samples (n=3) could not be conclusively determined. Our results suggest that there have been significant introductions of non-native M. galloprovincialis lineages into both southern and northern hemisphere populations.

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Comparing divergence landscapes from reduced-representation and whole-genome re-sequencing in the yellow-rumped warbler (Setophaga coronata) species complex

10.1101/2021.03.23.436663 ◽

2021 ◽

Author(s):

Stephanie Szarmach ◽

Alan Brelsford ◽

Christopher C Witt ◽

David Toews

Keyword(s):

Species Complex ◽

Mitochondrial Gene ◽

Model Organisms ◽

Whole Genome ◽

Sequencing Data ◽

Reduced Representation ◽

Mitochondrial Haplotypes ◽

Trade Offs ◽

Sequencing Method ◽

The Cost

Researchers seeking to generate genomic data for non-model organisms are faced with a number of trade-offs when deciding which method to use. The selection of reduced representation approaches versus whole genome re-sequencing will ultimately affect the marker density, sequencing depth, and the number of individuals that can multiplexed. These factors can affect researchers' ability to accurately characterize certain genomic features, such as landscapes of divergence-how FST varies across the genomes. To provide insight into the effect of sequencing method on the estimation of divergence landscapes, we applied an identical bioinformatic pipeline to three generations of sequencing data (GBS, ddRAD, and WGS) produced for the same system, the yellow-rumped warbler species complex. We compare divergence landscapes generated using each method for the myrtle warbler (Setophaga coronata coronata) and the Audubon's warbler (S. c. auduboni), and for Audubon's warblers with deeply divergent mtDNA resulting from mitochondrial introgression. We found that most high-FST peaks were not detected in the ddRAD dataset, and that while both GBS and WGS were able to identify the presence of large peaks, WGS was superior at a finer scale. Comparing Audubon's warblers with divergent mitochondrial haplotypes, only WGS allowed us to identify small (10-20kb) regions of elevated differentiation, one of which contained the nuclear-encoded mitochondrial gene NDUFAF3. We calculated the cost per base pair for each method and found it was comparable between GBS and WGS, but significantly higher for ddRAD. These comparisons highlight the advantages of WGS over reduced representation methods when characterizing landscapes of divergence.

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Reuniting males and females: redescriptions of Nuisiana arboris (Marples 1959) and Cambridgea reinga Forster & Wilton 1973 (Araneae: Desidae, Stiphidiidae)

Zootaxa ◽

10.11646/zootaxa.2739.1.4 ◽

2011 ◽

Vol 2739 (1) ◽

pp. 41 ◽

Cited By ~ 8

Author(s):

COR J. VINK ◽

BRIAN M. FITZGERALD ◽

PHIL J. SIRVID ◽

NADINE DUPÉRRÉ

Keyword(s):

Mitochondrial Dna ◽

New Zealand ◽

Cytochrome C ◽

Cytochrome C Oxidase ◽

Dna Sequences ◽

Mitochondrial Gene ◽

Junior Synonym ◽

Morphological Evidence ◽

Spider Species ◽

Males And Females

Two New Zealand endemic spider species, Nuisiana arboris (Marples 1959) (Desidae) and Cambridgea reinga Forster & Wilton 1973 (Stiphidiidae), are redescribed, including notes on their distribution and DNA sequences from the mitochondrial gene cytochrome c oxidase subunit 1. Based on morphological evidence and mitochondrial DNA sequences, Matachia magna Forster 1970 is a junior synonym of Nuisiana arboris, and Nanocambridgea grandis Blest & Vink 2000 is a junior synonym of Cambridgea reinga. Two forms of male morph in C. reinga are recorded.

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